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ABSTRACT: Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4,795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 04/2013; · 3.22 Impact Factor
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ABSTRACT: Respiratory syncytial virus (RSV) is a major cause of acute respiratory infections (ARIs) in children worldwide and can cause high mortality, especially in developing countries. However, information on the clinical and molecular characteristics of RSV infection in developing countries is limited. From April 2010 to May 2011, 1,082 nasopharyngeal swabs were collected from children with ARI admitted to the Children's Hospital 2, Ho Chi Minh City, Vietnam. Samples were screened for RSV and genotyped by reverse transcription-PCR and sequencing. Demographic and clinical data was also recorded. RSV was found in 23.8% (257/1,082) of samples. RSV A was the dominant subgroup, accounting for 91.4% (235/257), followed by RSV B, 5.1% (13/257), and 9 cases (3.5%) were mixed infection of these subgroups. The phylogenetic analysis revealed that all group A strains belonged to the GA2 genotype. All group B strains belonged to the recently identified BA genotype, and further clustered into 2 recently described subgenotypes BA9 and BA10. One GA2 genotype strain had a premature stop codon which shortened the G protein length. RSV infection was significantly associated with younger age and higher severity score than those without. Co-infection with other viruses did not affect disease severity. RSV A caused more severe disease than RSV B. The results from this study will not only contribute to the growing database on the molecular diversity of RSV circulating worldwide but may be also useful in clinical management and vaccine development.
PLoS ONE 01/2013; 8(1):e45436. · 4.09 Impact Factor
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Yuki Matsushima,
Hideaki Shimizu,
Atsuko Kano,
Etsuko Nakajima,
Yoko Ishimaru,
Shuvra Kanti Dey,
Yuki Watanabe,
Fuyuka Adachi,
Kohnosuke Mitani,
Tsuguto Fujimoto,
Tung Gia Phan, Hiroshi Ushijima
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ABSTRACT: A novel virus of the species human adenovirus D, HAdV-67 (P-New/H9/F25), was first isolated from diarrheal feces of six children in Dhaka City, Bangladesh. The genome of this novel virus may be composed of multiple recombinations among HAdV-9, HAdV-25, HAdV-26, HAdV-33, HAdV-46, and an unknown human adenovirus D which was an origin of HAdV-67.
Genome announcements. 01/2013; 1(1).
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Pattara Khamrin,
Aksara Thongprachum,
Hideaki Kikuta,
Atsuko Yamamoto,
Shuichi Nishimura,
Kumiko Sugita,
Tsuneyoshi Baba,
Masaaki Kobayashi,
Shoko Okitsu,
Satoshi Hayakawa,
Hiroyuki Shimizu,
Niwat Maneekarn, Hiroshi Ushijima
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ABSTRACT: Saffold virus (SAFV) is a newly discovered human virus in the genus Cardiovirus, family Picornaviridae. The virus was first described from fecal specimens of a child with fever of unknown origin in 2007. A total of 454 fecal specimens were collected from children with diarrhea attended clinics in Japan, 2010-2011, 7 (1.5%) were positive for SAFV. Mixed-infections of SAFV and other enteric viruses (rotavirus, norovirus, and bocavirus) were found in 4 out of 7 cases, while monoinfection by SAFV alone was detected in 3 cases. In addition to diarrhea, fever and vomiting were observed in 3 children and mild dehydration in 1 case. No particular symptoms of cough and rhinorrhea were noted. Analysis of partial VP1 nucleotide sequence of 7 Japanese SAFV strains revealed that 5 SAFV sequences were most closely related with SAFV2 reference strains, but separated into SAFV2-A (3 strains) and SAFV2-B (2 strains). In addition, the other 2 strains were classified as SAFV3. Our results indicated that SAFVs (SAFV2 and SAFV3) were circulated in children with acute gastroenteritis in Japan during 2010 and 2011 epidemic season.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 11/2012; · 3.22 Impact Factor
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ABSTRACT: The postnatal transmission of human immunodeficiency virus (HIV) from mothers to children occurs through breastfeeding. Although heat treatment of expressed breast milk is a promising approach to make breastfeeding safer, it is still not popular, mainly because the recommended procedures are difficult to follow, or time-consuming, or because mothers do not know which temperature is sufficient to inactivate HIV without destroying the nutritional elements of milk. To overcome these drawbacks, a simple and rapid method of heat treatment that a mother could perform with regular household materials applying her day-to-day art of cooking was examined. This structured experiment has demonstrated that both cell-free and cell-associated HIV type 1 (HIV-1) in expressed breast milk could be inactivated once the temperature of milk reached 65°C. Furthermore, a heating method as simple as heating the milk in a pan over a stove to 65°C inhibited HIV-1 transmission retaining milk's nutritional key elements, for example, total protein, IgG, IgA, and vitamin B(12) . This study has highlighted a simple, handy, and cost-effective method of heat treatment of expressed breast milk that mothers infected with HIV could apply easily and with more confidence. J. Med. Virol. © 2012 Wiley Periodicals, Inc.
Journal of Medical Virology 11/2012; · 2.82 Impact Factor
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ABSTRACT: This study examined the virucidal effects of five types of alcohol-based sanitizers including malic acid and sodium malate, or monoethanolamin, in 58 vol % ethanol (pH 4.0, pH 7.1, pH 11.8), 65 vol % ethanol (pH 4.2), and 75 vol % ethanol (pH 4.4) against murine norovirus (MNV) and feline calicivirus (FCV). The virus titer of MNV was reduced in an ethanol dose-dependent manner under the same pH (about 4.0) condition. Virucidal effect against MNV was correlated with pH when the concentration of ethanol was constant (58 vol %). All the ethanol-based sanitizers provided sufficient virucidal effects against FCV. In conclusion, the virucidal effect of the ethanol-based sanitizer at low concentration of ethanol against norovirus (NoV) is increased when the pH is adjusted to a neutral state.
Journal of Infection and Chemotherapy 11/2012; · 1.80 Impact Factor
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ABSTRACT: Human astrovirus (HAstV) is one of the causative agents of acute gastroenteritis in children worldwide. The objective of this study was to elucidate the molecular epidemiology and genotypic diversity of HAstV circulating in pediatric patients admitted to hospital with diarrhea in Thailand during the year 2000-2011, except for 2004, 2006, and 2009. A total of 1,022 fecal specimens were tested for HAstV by reverse transcription polymerase chain reaction (RT-PCR). HAstV was detected at 1.4% (14 of 1,022). All HAstV strains detected in this study were characterized further by nucleotide sequencing and phylogenetic analysis. Analysis of 348 bp partial capsid nucleotide sequences revealed that HAstV strains detected were HAstV-1 (1a, 1b, and 1d) (8 strains), HAstV-2 (2c) (3 strains), HAstV-3 (1 strain), and HAstV-5 (2 strains). HAstV-1, the most predominant genotype was detected initially in 2002 and circulated continuously up to 2011. HAstV-2 was detected in year 2001, and 2007 and grouped into a 2c lineage. HAstV-3 was found only in 2000 and HAstV-5 was found in the year 2001. The findings indicate that a wide variety of HAstV strains continue to circulate in children admitted to hospital with acute gastroenteritis in Thailand over a decade. The data provide an epidemiological overview of HAstV infection and HAstV genotype distribution in Thailand. J. Med. Virol. 84:1751-1756, 2012. © 2012 Wiley Periodicals, Inc.
Journal of Medical Virology 11/2012; 84(11):1751-6. · 2.82 Impact Factor
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Aksara Thongprachum,
Wisoot Chan-It,
Pattara Khamrin,
Shoko Okitsu,
Shuichi Nishimura,
Hideaki Kikuta,
Atsuko Yamamoto,
Kumiko Sugita,
Tsuneyoshi Baba,
Masashi Mizuguchi,
Niwat Maneekarn,
Satoshi Hayakawa, Hiroshi Ushijima
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ABSTRACT: The molecular epidemiology and characterization of rotaviruses obtained from non-hospitalized children with acute gastroenteritis in five different prefectures (Hokkaido, Saga, Tokyo, Osaka, and Kyoto) from July 2009 to June 2011 was investigated. Among 831 fecal specimens tested, rotavirus was found in 165 specimens (19.9%). The rotavirus detection rate in 2010-2011 (23.3%) was higher than those in 2009-2010 (16.0%). The highest prevalence of rotavirus was found in children aged 12 to 23 months. Rotavirus could be detected throughout the 8-month period with a peak in April. We found that G3P[8] was the most prevalent genotype (54.5%), followed by G1P[8] (29.1%), G9P[8] (9.1%), G3P[4] (3.0%), G2P[4] (2.5%), G1P[4] (1.2%), and G4P[8] (0.6%), respectively. Interestingly, G3 strains emerged as the most predominant genotype and replaced G1 rotavirus which had been reported as the most predominant genotype in the previous studies. Phylogenetic analysis revealed that G3 rotavirus strains were closely related to the "new variant G3" 5091 strain, which emerged in Japan in 2003-2004. A significant increase in the prevalence of rotavirus G3 found in this study indicates that rotavirus G3 strain is the major cause of infection in five geographical areas of Japan and may distribute globally in the near future.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 10/2012; · 3.22 Impact Factor
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ABSTRACT: A total of 463 fecal specimens from human patients were tested for the presence of Camphylobacter by a commercial immunochromatography kit (ImmunoCard STAT! CAMPY), polymerase chain reaction (PCR) and conventional bacteriological (CB) methods. Using culture as the standard of reference, the ImmunoCard STAT! CAMPY assay had a sensitivity of 86% and a specificity of 100%. On the other hand, using PCR as the standard of reference, ImmunoCard STAT! CAMPY assay had a sensitivity of 90.5% and a specificity of 100%.
Journal of microbiological methods 10/2012; · 2.43 Impact Factor
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Quang Duy Trinh,
Ngan Thi Kim Pham,
Nhut Tin Le Nguyen,
Bao Quoc Lam,
Kim Thoa Le Phan,
Khanh Huu Truong,
Thinh Quoc Le,
Hung Thanh Nguyen,
Thuong Chi Tang,
Yasuyuki Izumi,
Shihoko Komine-Aizawa, Hiroshi Ushijima,
Satoshi Hayakawa
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ABSTRACT: A total of 89 blood samples collected from HIV-infected infants and children from provinces of southern Vietnam who were hospitalized at Children's Hospital 1, Ho Chi Minh City, during the 1-year period from October 2004 to September 2005 were submitted to serological screening for IgG, IgA, and IgM antibodies against Chlamydophila pneumoniae (C. pneumoniae). The presence of this microorganism was also evaluated by PCR. The results showed that 64 % of the samples were positive for anti-C. pneumoniae IgG, 31.5 % were positive for IgA, and 3.4 % were positive for IgM. The highest prevalences of IgG and IgA positivity, 75 % and 66.7 %, respectively, were noted in the 1- to 2-year-old age group. However, all the samples were negative for C. pneumoniae by PCR. The study revealed a high seroprevalence of C. pneumoniae in Vietnamese infants and children with HIV/AIDS.
Journal of Infection and Chemotherapy 10/2012; · 1.80 Impact Factor
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ABSTRACT: Human adenovirus type 8 (HAdV-8) is a major causative agent of epidemic keratoconjunctivitis, which is frequently associated with community, industrial and nosocomial outbreaks. Restriction endonuclease (RE) analysis discriminates HAdV-8 isolates into genome types, making it possible to correlate between genomic variants, virulence and outbreak potential. RE analysis is performed using two sets of classification criteria, an Asian and a European system. So far, genome types HAdV-8A-8K and HAdV-8/D1-D12 have been included in the Asian and European classifications, respectively. Conventionally followed RE analysis has some inherent problems, such as the use of a neutralization test for HAdV-8 typing, which may misidentify some recombinant adenoviruses as HAdV-8 due to cross-reaction, the lack of a complete restriction profile for all genome types for purposes of comparison, and the absence of enzyme codes in the Asian classification system. In this review, we propose typing of HAdV-8 with phylogenetic analysis of the hexon and fibre genes prior to RE analysis due to the emergence of many recombinant types. Schematic restriction profiles for both classification systems were created by compiling all the published reports on genome types, and enzyme codes were included for the Asian classification system. The updated and simplified stepwise approach for HAdV-8 genome typing presented here could be useful for identifying either existing genome types or novel ones.
Journal of Medical Microbiology 09/2012; 61(Pt 11):1491-503. · 2.50 Impact Factor
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ABSTRACT: A rare human G10P[8] rotavirus with a reassortment between bovine and human viruses was detected from a patient with acute gastroenteritis in Vietnam. Genetic analysis using complete coding sequences of all segments showed a genomic constellation of this virus of G10-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Its VP7 region was genetically related to that of a bovine rotavirus derived from Australia (strain VICG10.01), whereas all other genes were identical to those of a human rotavirus derived from Australia (strain Victoria/CK00047). These results indicate a possibility that the reassortment of the rotavirus was caused by immune escape in Australia and the rotavirus was carried to Vietnam. Additionally, this finding will help further understanding the evolution of rotaviruses circulating in Vietnam.
Journal of Virology 09/2012; 86(18):10236-7. · 5.40 Impact Factor
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ABSTRACT: Several epidemiological studies reported the detection of rotavirus strains bearing unusual combinations of genetic background of human and porcine rotaviruses. This observation supports the hypothesis of interspecies transmission of rotaviruses in humans and pigs. The aims of this study were to investigate the genotypes and molecular characteristics of rotaviruses in piglets with diarrhea in several farms from two provinces in Thailand. A total of 207 fecal specimens collected from diarrheic piglets were screened for the presence of groups A, B, and C rotaviruses. Group A rotaviruses were detected in 41 out of 207 (19.8%) fecal specimens tested. A wide variety of G-P combination rotavirus strains were detected in this study. The G4P[6] was identified as the most prevalent genotype (39.0%), followed by G4P[23] (12.2%), G3P[23] (7.3%), G4P[19] (7.3%), G3P[6] (4.9%), G3P[13] (4.9%), G3P[19] (4.9%), G9P[13] (4.9%), G9P[19] (4.9%), G5P[6], and G5P[13] each of 2.4%. Furthermore, G5 and G9 in combinations with P-nontypeable strains were also found at each consisting of 2.4% (n=1) of the collection. It was interesting to note that among diversified porcine rotavirus strains, novel combinations of G4P[19] and G9P[19] strains were detected for the first time in this study. Nucleotide sequences of VP4 and VP7 of these strains were closely related to human rotaviruses reported previously. The data implies that these porcine rotaviruses were probably generated in nature from the reassortment between the viruses of human and porcine origin. This study provides valuable epidemiological information and molecular characteristics of porcine rotaviruses circulating in piglets with diarrhea in northern Thailand.
Veterinary Microbiology 07/2012; · 3.33 Impact Factor
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ABSTRACT: Norovirus (NoV) is recognized as one of the most common causative agents of diarrhea disease in young children. A total of 187 fecal specimens collected from non-hospitalized children with acute gastroenteritis in Shizuoka, Japan during July 2008 to June 2009 were investigated for the presence of diarrhea viruses by a multiplex RT-PCR. Diarrhea viruses were overall detected in 158 of 187 (84.5%). Of the viruses detected, NoV was the most prevalent (55.6%). Most of the NoV sequences belonged to GII.4 (53.8%). NoV GII.6 emerged as the second most common strain (40.4%). The full-length capsid sequences of five representative Shizuoka GII.6 strains were compared with all 12 GII.6 strains available in GenBank database between 1990 and 2009. At least three distinct GII.6 subclusters (a-c) appeared in different parts of the world. Shizuoka GII.6 strains formed their own subcluster c, distinct from other complete GII.6 reference sequences. The Shizuoka strains had significant amino acid divergence, particularly in the P2 domain up to 10.9-17.5% and contained eight unique mutations in the P domains, compared with subcluster a and b viruses. The homology model showed that the eight mutations were predicted to be located at the surface-exposed P1 and P2 domains. The data suggest the emergence of a new NoV GII.6 variant in Shizuoka, with a high level of genetic variation.
Journal of Medical Virology 07/2012; 84(7):1089-96. · 2.82 Impact Factor
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ABSTRACT: This study reports the detection and the genetic characterization of HBoV, a new member in the Parvoviridae family. Among 177 fecal specimens collected from children with diarrhea younger than 5 years in Japan, 11 (6.2%) were positive for HBoV. Co-infection with other enteric viruses (norovirus and adenovirus) was found in nine (81.8%) pediatric patients, while monoinfection by HBoV alone was detected in two (18.2%) cases. Nucleotide sequence analysis of 11 Japanese HBoV strains revealed that seven HBoV sequences were most closely related to other HBoV 1 reference strains, while the other four strains were similar to HBoV 2A. These results indicated that HBoV was one of the viral agents found in stool specimens collected from children with acute gastroenteritis and HBoV 1 and 2A circulated in Japan between 2009 and 2010 epidemic season.
Journal of Medical Virology 06/2012; 84(6):901-5. · 2.82 Impact Factor
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ABSTRACT: Rotavirus is a major cause of morbidity and mortality of infants and young children with diarrhea throughout the world. In Thailand, extensive studies of rotavirus infections have been reported continually and rotavirus diarrhea remains a common illness. To monitor the epidemiological situation of rotavirus in Chiang Mai, Thailand, surveillance of rotavirus circulating in pediatric patients was conducted. A total of 160 fecal specimens collected from children hospitalized with diarrhea were tested for rotaviruses groups A, B, and C by RT-PCR and their genotypes were identified by multiplex PCR and nucleotide sequencing. Group A rotavirus was detected at 29.4% but none of group B and C was found in this study. Molecular characterizations of G- and P-genotypes revealed three different G-P combinations, G1P[8] was the most predominant genotype with the prevalence of 72.3% followed by G2P[4] at 19.2%, and G3P[8] at 8.5%. Phylogenetic analyses of VP7 and VP4 genes of the representative strains detected in the present study, G1, G2, G3, and P[4] and P[8], respectively, revealed that G1 belonged to G1-Ic and G1-II, G2 belonged to G2-II, and G3 belonged to G3-III-S4 lineages while P[4] and P[8] were identified as P[4]-V and P[8]-III lineages. Analyses of VP6, NSP4, and NSP5 genes demonstrated that these representative strains belonged to genotypes I1 and I2, E1 and E2, and H1 and H2, respectively. Analyzing the association of G- and P-genotypes with I, E, H genotypes revealed unique patterns of genotypic linkage. The G1P[8] and G3P[8] were intimately linked with I1, E1, H1 genotypes and displayed the genetic features of G1-P[8]-I1-E1-H1 and G3-P[8]-I1-E1-H1, respectively, while G2P[4] was closely linked to I2, E2, H2 genotypes and showed the genetic pattern of G2-P[4]-I2-E2-H2. This study provides epidemiological information and insight into the genetic background of rotaviruses circulating in pediatric patients in Chiang Mai, Thailand.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 05/2012; 12(7):1381-91. · 3.22 Impact Factor
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Yuki Matsushima,
Hideaki Shimizu,
Atsuko Kano,
Etsuko Nakajima,
Yoko Ishimaru,
Shuvra Kanti Dey,
Yuki Watanabe,
Fuyuka Adachi,
Keiichiro Suzuki,
Kohnosuke Mitani,
Tsuguto Fujimoto,
Tung Gia Phan, Hiroshi Ushijima
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ABSTRACT: We report a novel human adenovirus D (HAdV-65) isolated from feces of 4 children in Bangladesh who had acute gastroenteritis. Corresponding genes of HAdV-65 were related to a hexon gene of HAdV-10, penton base genes of HAdV-37 and HAdV-58, and a fiber gene of HAdV-9. This novel virus may be a serious threat to public health.
Emerging Infectious Diseases 05/2012; 18(5):846-8. · 6.79 Impact Factor
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ABSTRACT: Rubella virus (RV) usually causes a mild disease. However, infection during the first trimester of pregnancy often leads to severe birth defects known as congenital rubella syndrome (CRS). Although wild-type RVs exist and circulate worldwide, their genotypes remain unknown in many countries. The aim of this study was to identify the molecular characteristics of RVs found in Vietnam during the years 2009-2010 and to provide the first data concerning RV genotypes in this country. Throat swab samples were collected between 2009 and 2010 from four CRS cases and nine rubella infection cases visiting one Children's Hospital and one outpatient clinic in Ho Chi Minh City. The 739-nucleotide coding region of the RV E1 gene recommended by the World Health Organization was amplified by reverse transcriptase PCR, and the resulting DNA fragments were then sequenced. Sequences were assigned to genotypes by phylogenetic analysis with RV reference strains. RV RNA was detected in 11 clinical specimens. Phylogenetic analysis of the sequences showed that all 11 strains belonged to 2B genotype. Several variations in amino acids were found, among which five changes were involved in the B and T cell epitopes. These data indicate that viruses of genotype 2B were circulating in Vietnam. The increasing information about RV genotype in Vietnam should aid in the control of rubella infection and CRS in this country.
Journal of Medical Virology 04/2012; 84(4):705-10. · 2.82 Impact Factor
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Quang Duy Trinh,
Ngan Thi Kim Pham,
Nhut Tin Le Nguyen,
Bao Quoc Lam,
Kim Thoa Le Phan,
Khanh Huu Truong,
Yasuyuki Izumi,
Shihoko Komine-Aizawa,
Masashi Mizuguchi, Hiroshi Ushijima,
Satoshi Hayakawa
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ABSTRACT: Abstract Anti-HIV drugs have recently become available for the treatment of children infected with HIV in Vietnam; however, the genetic background of HIV-1 drug resistance in antiretroviral-naive children has yet to be studied. Of the 104 HIV-1 CRF01-AE subtype strains that were previously isolated from antiretroviral-naive children from the provinces of southern Vietnam and hospitalized in Children Hospital 1 in Ho Chi Minh City from 2004 to 2005, 79 strains were used for amplification and sequence analyses of the protease and reverse transcriptase (RT) genes. Minor mutations were found in the protease gene, including L10I, I13V, G16E, M36I, D60E, I62V, I64V, L63P, H69K, V82I, and I93L. Of these mutations, M36I and H69K were detected in all of the strains that were studied. However, all of the amino acid changes in the protease gene were considered to be polymorphisms. In the RT gene, three major mutations were detected in six strains: the V75M mutation in one strain, the Y181C mutation in two strains, and the M184I mutation in three strains. The prevalence of primary or transmitted HIV drug resistance to all of the drugs and drug classes that were evaluated in this study was 7.6%. These findings provide a useful background for antiretroviral therapy in Vietnam and contribute reference data for the surveillance of HIV drug resistance around the world. This study suggests that the prevalence of HIVDR in Vietnam may have recently increased. The monitoring of HIV drug resistance in Vietnam is necessary.
AIDS research and human retroviruses 03/2012; 28(10):1305-7. · 2.18 Impact Factor
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ABSTRACT: Rubella virus (RUBV), a small, plus-strand RNA virus that is an important human pathogen, has the unique feature that the GC content of its genome (70%) is the highest (by 20%) among RNA viruses. To determine the effect of this GC content on genomic evolution, base and codon usage were analyzed across viruses from eight diverse genotypes of RUBV. Despite differences in frequency of codon use, the favored codons in the RUBV genome matched those in the human genome for 18 of the 20 amino acids, indicating adaptation to the host. Although usage patterns were conserved in corresponding genes in the diverse genotypes, within-genome comparison revealed that both base and codon usages varied regionally, particularly in the hypervariable region (HVR) of the P150 replicase gene. While directional mutation pressure was predominant in determining base and codon usage within most of the genome (with the strongest tendency being towards C's at third codon positions), natural selection was predominant in the HVR region. The GC content of this region was the highest in the genome (>80%), and it was not clear if selection at the nucleotide level accompanied selection at the amino acid level. Dinucleotide frequency analysis of the RUBV genome revealed that TpA usage was lower than expected, similar to mammalian genes; however, CpG usage was not suppressed, and TpG usage was not enhanced, as is the case in mammalian genes.
Archives of Virology 02/2012; 157(5):889-99. · 2.11 Impact Factor
